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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN-SPECIFIC TOXIN INTERMEDILYSIN
 
Authors :  G. Polekhina, K. S. Giddings, R. K. Tweten, M. W. Parker
Date :  14 Jan 04  (Deposition) - 25 Jan 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  A,B  (2x)
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Polekhina, K. S. Giddings, R. K. Tweten, M. W. Parker
Insights Into The Action Of The Superfamily Of Cholesterol-Dependent Cytolysins From Studies Of Intermedilysin
Proc. Natl. Acad. Sci. Usa V. 102 600 2005
PubMed-ID: 15637162  |  Reference-DOI: 10.1073/PNAS.0403229101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERMEDILYSIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTRCHISA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOCOCCUS INTERMEDIUS
    Organism Taxid: 1338

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB
Biological Unit 4 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 4 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:92 , LEU A:440 , ARG A:477 , HOH A:1035 , HOH A:1058 , LYS B:87BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARELYS A:87 , ASN A:88 , ARG B:477BINDING SITE FOR RESIDUE SO4 A 1002
3AC3SOFTWAREILE A:450 , ARG A:477 , LYS B:87 , ASN B:88 , HOH B:1193BINDING SITE FOR RESIDUE SO4 B 1003
4AC4SOFTWARELYS A:87 , ARG B:92 , LEU B:440 , ARG B:477 , HOH B:1169BINDING SITE FOR RESIDUE SO4 B 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S3R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S3R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S3R)

(-) Exons   (0, 0)

(no "Exon" information available for 1S3R)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:473
 aligned with Q9LCB8_STRIT | Q9LCB8 from UniProtKB/TrEMBL  Length:532

    Alignment length:473
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525   
         Q9LCB8_STRIT    56 NSEAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSKLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPSNSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVDFSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNVSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEASKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYKDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVRNIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVK 528
               SCOP domains d1s3ra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1s3rA01                 1s3rA02 A:80-115,A:401-417          1s3rA01 A:56-79,A:116-203,A:257-300,A:377-400 HIV-1 Reverse Transcriptase; Chain        -----------------------------------------------------1s3rA01 HIV-1 Reverse Transcriptase; Chain  ----------------------------------------------------------------------------1s3rA01                 1s3rA02          1s3rA04 A:418-528 Perfringolysin, domain 4                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.........eee..ee...eeeeeeee..eeeeeeeeeeeeeeee..ee....hhhhh....eee.hhhhhh............eeeee..........eeee...hhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..hhhhhhhhhh.hhhhhhhhhh.hhhhhhh...eeeeeeeeeeeeeeee....hhhhhh....hhhhhhhh.......eeeeeeeeeeeeeeeeeee.....hhhhhhhhhhh.........hhhhhh...eeeeee.........eeeehhhhhhhhhhhh.........eeeeeeeee........eeeeeeeeeeeeeeee.eeeeeee.....eeeeeeeeeeee.....eeeeeee............eeeeee...eeeeeeeeeee.......eeeeeeeeee....eeeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s3r A  56 NSEAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSKLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPSNSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVDFSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNVSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEASKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYKDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVRNIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVK 528
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525   


Chain B from PDB  Type:PROTEIN  Length:473
 aligned with Q9LCB8_STRIT | Q9LCB8 from UniProtKB/TrEMBL  Length:532

    Alignment length:473
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525   
         Q9LCB8_STRIT    56 NSEAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSKLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPSNSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVDFSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNVSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEASKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYKDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVRNIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVK 528
               SCOP domains d1s3rb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1s3rB01                 1s3rB02 B:80-115,B:401-417          1s3rB01 B:56-79,B:116-203,B:257-300,B:377-400 HIV-1 Reverse Transcriptase; Chain        -----------------------------------------------------1s3rB01 HIV-1 Reverse Transcriptase; Chain  ----------------------------------------------------------------------------1s3rB01                 1s3rB02          1s3rB04 B:418-528 Perfringolysin, domain 4                                                                      CATH domains
           Pfam domains (1) ----Thiol_cytolysin-1s3rB01 B:60-526                                                                                                                                                                                                                                                                                                                                                                                                                                                   -- Pfam domains (1)
           Pfam domains (2) ----Thiol_cytolysin-1s3rB02 B:60-526                                                                                                                                                                                                                                                                                                                                                                                                                                                   -- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhh...hhhhhheee.......ee..eeee..eeeeeeeeeeeeeeee..ee.............eee.hhhhhh............eeeee..........eeee...hhhhhhhhhhhhhhhhhhhhh.......eeeeeeee..hhhhhhhhhh.hhhhhhhhhh.hhhhhhh...eeeeeeeeeeeeeeee....hhhhhh....hhhhhhhh.......eeeeeeeeeeeeeeeeeee.....hhhhhhhhhhh........hhhhhhhheeeeeeee..........eeehhhhhhhhhhhh.........eeeeeeeee........eeeeeeeeeeeeeeee.eeeeeee......eeeeeeeeeee.....eeeeeee............eeeeee...eeeeeeeeeee.......eeeeeee.......eeeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s3r B  56 NSEAAKKALNDYIWGLQYDKLNILTHQGEKLKNHSSREAFHRPGEYVVIEKKKQSISNATSKLSVSSANDDRIFPGALLKADQSLLENLPTLIPVNRGKTTISVNLPGLKNGESNLTVENPSNSTVRTAVNNLVEKWIQNYSKTHAVPARMQYESISAQSMSQLQAKFGADFSKVGAPLNVDFSSVHKGEKQVFIANFRQVYYTASVDSPNSPSALFGSGITPTDLINRGVNSKTPPVYVSNVSYGRAMYVKFETTSKSTKVQAAIDAVVKGAKLKAGTEYENILKNTKITAVVLGGNPGEASKVITGNIDTLKDLIQKGSNFSAQSPAVPISYTTSFVKDNSIATIQNNTDYIETKVTSYKDGALTLNHDGAFVARFYVYWEELGHDADGYETIRSRSWSGNGYNRGAHYSTTLRFKGNVRNIRVKVLGATGLAWEPWRLIYSKNDLPLVPQRNISTWGTTLHPQFEDKVVK 528
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: CDC (6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9LCB8_STRIT | Q9LCB8)
molecular function
    GO:0015485    cholesterol binding    Interacting selectively and non-covalently with cholesterol (cholest-5-en-3-beta-ol); the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.

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 Related Entries

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UniProtKB/TrEMBL
        Q9LCB8_STRIT | Q9LCB8: 4bik 5imt 5imw

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